Answer: Oh yeah, unfortunately, this is a problem. If you had mushrooms sprouting in your soil, it was not sterile to begin with. If you purchased it, I would return any leftovers and ask for a refund. Sterile soil should not contain mushroom spores. Sterile soil also would not contain the organisms that result in the black spots on your tomatoes. What about the containers you are growing in? Are you absolutely positive they were sterile? Sterilize them by washing first in soapy water and then, rinse in a solution of 1 part bleach to 10 parts water and allow to air dry. It does sound like your soil may have been too wet as well. Keep an eye on watering, don't let your soil dry out but never let it get to the point it could be considered "wet" either. What about the air circulation in the basement? Seedlings need very good air circulation to head off fungal diseases. Consider placing a fan in the basement, not directly on the seedlings but enough wind to stir the air up a bit. Also, the cool temperatures and dampness in most basements can stress and stunt seedlings, inviting problems. I would start some more tomatoes and try to improve the situation for the other seedlings using the above suggestions.
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